TavernaTaverna workflow system2015-08-02T21:27:40Zhttp://www.taverna.org.uk/feed/atom/adminhttp://www.taverna.org.uk/2015/03/04/google-summer-of-code-taverna-projects/2015-08-02T21:27:38Z2015-03-04T10:35:34ZThe Apache Software Foundation has been accepted as a mentoring organization for the 2015 Google Summer of Code[1]. The full list of Apache GSOC projects[2] includes four Taverna-related projects[3] : a production-suitable command line tool, a databundle viewer, OGC WPS support and an Android App for Taverna.

A production-suitable command line tool [4]=======================================

This proposed GSOC project is to formalize the command line interface for Taverna Language so that it can achieve some of the below:

a) In collaboration with dev@taverna and the mentor, define command line options for workflow conversions and inspectionb) Find and use an appropriate command line parser libraryc) –helpd) Basic error handling (e.g. file not found)e) Batch processing – e.g. recursive conversionsf) Arguments for choosing input and output formatsg) Unit and Integration Tests for the above (ideally through Maven)The project can be extended by exposing other parts of the API that don't currently have a command line equivalent, e.g.h) Workflow validationi) Workflow statistics (number of processors, links, etc)

A databundle viewer [5]===================

This GSOC project proposes to create a web-based presentation (but not edit) of a workflow run, e.g. the following user story:

1) User uploads the databundle file for a workflow run (or provides the URI to one existing elsewhere) into the presentation system2) The presentation system shows basic information about the workflow run3) User navigates to inputs/outputs4) The presentation system presents a list of inputs or outputs – embedding images etc. where possible, download links for large files, inline for small text, etc5) User downloads a selected data file

Metadata provided can be presented in many different ways, for instance:

a) Which workflow was executed?b) Which steps were executed?c) What step produced this value?d) What values were produced by this step?e) What steps used this value?

OGC WPS support [6]===============

This proposed GSOC project is to, in collaboration with dev@taverna and the mentor

(a) Improve/complete the existing Taverna 2.5 WPS prototype support Discovery of WPS services from a user-specified WPS server Configuration of WPS services Execution of WPS services(b) Test WPS support using pre-selected WPS servers and services(c) Migrate the WPS support to the Taverna 3 codebase(c) Document the Taverna 3 WPS service support

An Android App for Taverna [7]==========================

The project would be to:

Extend and complete Taverna Mobile: an Android app to run Tavernaworkflows available on myExperiment (http://www.myexperiment.org)using Taverna Server.

1) fix the ssl/https parts and use the latest version of taverna server2) update the code to remove some legacy dependencies and use thelatest APIs3) improve the UI and responsiveness

============================

If you, or any students you know, are interested in these or any other Taverna projects, then please discuss ideas on the Taverna developers' list dev@taverna.incubator.apache.org and then submit proposals to Google by 27th March. More information is in the GSOC 2015 FAQ [8]

]]>0adminhttp://prototype.taverna.org.uk/2015/02/23/apache-officially-given-control-of-taverna/2015-08-02T21:27:39Z2015-02-23T10:30:18ZThe University of Manchester has now officially granted control of the Taverna source code to the Apache Software Foundation. The source code is now at git://git.apache.org/incubator-taverna-engine.git etc.﻿

]]>0adminhttp://prototype.taverna.org.uk/2014/12/04/astrotaverna-building-workflows-with-virtual-observatory-services/2015-08-02T21:27:39Z2014-12-04T16:18:39ZJ E Ruiz et al. has published this article about the AstroTaverna plugin and how it integrates existing Virtual Observatory web services as first-class building blocks in Taverna workflows.

The AstroTaverna plugin is included in the Astronomy releases for Taverna 2.5﻿

]]>0adminhttp://prototype.taverna.org.uk/2014/11/30/modelling-the-sun-with-taverna/2015-08-02T21:27:40Z2014-11-30T23:15:50ZPierantoni et al. has published this article about combining Taverna workflows from myExperiment to build heliophysics propagation models, reusing workflows from the helio-vo.eu project.The final workflow is shared at http://www.myexperiment.org/workflows/4055﻿

]]>0adminhttp://prototype.taverna.org.uk/2014/10/20/taverna-has-been-accepted-as-an-apache-incubator-project/2015-06-18T16:27:38Z2014-10-20T10:29:54ZThe Apache Software Foundation is a non-profit organization, forming a community of open-source software projects with strong emphasis on openness, collaboration and a consensus-based development process. Well-known Apache projects include the Apache HTTP server, Tomcat, Maven, Jena, CXF and OpenOffice.

Practically, this means that the Taverna code base, mailing lists and website will be migrated to the Apache infrastructure, and future releases will be called Apache Taverna.

Apache Taverna development will follow a clear open process, with important decisions (such as approving a release) done by voting on the new dev@taverna.incubator.apache.org mailing list, which will be open to anyone.

The Taverna team is thrilled by this move, and hope that this will encourage further involvement in Taverna project. At the Taverna Open Development workshop on the 30th of October 2014 we will discuss Apache Taverna in detail. http://taverna2014.eventbrite.co.uk/

Process Description – Apache Incubator
The incubation process covers the establishment of a candidate, acceptance (or rejection) of a candidate leading to the potential establishment of a Podling and associated incubation process, which ultimately leads to the establishment or a new Apache Top-Level-Project (TLP) or sub-project …

]]>0adminhttp://prototype.taverna.org.uk/2014/09/08/taverna-open-development-workshop-2014-10-30-2014-10-31/2015-05-26T21:27:27Z2014-09-08T14:08:43ZWe would like to invite you to the Taverna Open Development Workshop 2014, where we will focus on Taverna 3 and the move to an open development process.

Time and location:30. – 31. October 2014Room IT407, IT Building, School of Computer Science, University of Manchester, Manchester, M13 9PL, United Kingdom

This workshop is open to the wide community of Taverna developers, integrators and plugin makers, especially those who are interested in the upcoming Taverna 3 release, plugins and APIs, and in how to get started with the Taverna 3 codebase from Github.

If you are a regular user of Taverna (e.g. designing or running workflows), you are still welcome to participate, but please be aware that this is a workshop targeting software developers rather than scientists.

The event is free to attend. The University of Manchester will be providing lunch and refreshments, however transport and accommodation must be covered by the attendee. If you would like to attend this workshop, please register at http://taverna2014.eventbrite.co.uk/﻿

]]>0adminhttp://prototype.taverna.org.uk/2014/08/27/workflows-tutorial-at-eccb/2015-03-16T17:27:10Z2014-08-27T13:18:11ZDr Katy Wolstencroft will be co-presenting the "Scientific Workflows for Analysing, Integrating and Scaling Bioinformatics Data: a Practical Introduction to Galaxy, Taverna and WS-PGRADE" tutorial at the European Conference of Computational Biology ECCB'14.